The carbon stocks (Corg stocks) in mangrove sediments and the distribution and source changes of sedimented organic matter in Qinglan Bay are not understood as the mangrove forests decrease. In this paper, we collected two sediment cores in the interior mangrove and 37 surface sediment samples from mangrove-fringe, tidal flat and subtidal habitats and then analysed the total organic carbon (TOC), total nitrogen (TN), and the stable organic carbon isotope (δ13C) and nitrogen isotope (δ15N) in the sediment samples to obtain the organic matter sources and carbon stocks in two different mangrove sediment cores from Qinglan Bay. The δ13C and TOC/TN values showed that mangrove plants and algae were the main sources of organic matter. Relatively high contributions of mangrove plants (>50 %) were distributed in the mangrove areas in Wenchang estuary, the northern region of Bamen Bay and the eastern side of the Qinglan tidal inlet. The enriched δ15N values might be related to anthropogenic nutrient inputs, including increased aquaculture wastewater, human sewage and ship wastewater. The Corg stocks in cores Z02 and Z03 were 357.79 Mg C ha−1 and 265.78 Mg C ha−1, respectively. This Corg stock difference might have been related to the salinity and the benthos activities. The high Corg stock values measured in Qinglan Bay were caused by the mangrove maturity and stand age. The total Corg storage of the mangrove ecosystem in Qinglan Bay was estimated to be approximately 263.93 Gg C. This study contributes to organic carbon stocks and sources of sedimented organic matter in global mangroves.